RPSBLAST alignment for GI: 254780306 and conserved domain: cd00186

>gnl|CDD|73184 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.. Length = 381
 Score =  390 bits (1003), Expect = e-109
 Identities = 187/442 (42%), Positives = 245/442 (55%), Gaps = 67/442 (15%)

Query: 133 DLVNAYLARRALDYLVGFNLSPILWQKLPGAR--SAGRVQSVALRLICNRENQIESFVSE 190
           +LVNA LARR LD LVGFNLS +L +KL      SAGRVQS  L LI  RE +I++FV E
Sbjct: 2   NLVNAQLARRILDRLVGFNLSRLLTKKLRRKGVLSAGRVQSPTLGLIVEREREIKAFVPE 61

Query: 191 EYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENK 250
           +YW +                                                V  +E K
Sbjct: 62  DYWEIK--------------------------------------------EAVVVSVEKK 77

Query: 251 PIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVH 310
             K+NP P FTTSTLQQ ASS+LGFSA  TM+IAQKLYE         GLITY RTD   
Sbjct: 78  EKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA--------GLITYPRTDSTR 129

Query: 311 MSPDALEAVRRSITSHYGDHYLPEKPR---IYSSKSKNAQEAHEAIRPNDFDFLPSKMKQ 367
           +S +A+   R  I + YG  YL   P        + K  Q AHEAIRP        +++ 
Sbjct: 130 LSEEAILEAREYIQAIYGKEYLYPAPLLGRRNPKRGKKEQGAHEAIRPTKVAP-TPELEA 188

Query: 368 FLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKV 427
            L  D+F+LY LIW+R +ASQMA AK+E TTV +           + +G +L  DG+L+V
Sbjct: 189 NLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGGE----KFKASGKVLLEDGWLEV 244

Query: 428 WENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGR 487
           +      E+  +E+   P +   ++L   E    +  T+PPPRY+E+SLIK ME+ GIGR
Sbjct: 245 YP-----EEKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGR 299

Query: 488 PSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEI 547
           PSTYA+I+ETL  R YV  EK+K++P   G  V   LE  F + V+ +FTA LEEKLDEI
Sbjct: 300 PSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDEI 359

Query: 548 STGKLNWKEVLHEFWEEFIEKI 569
           + GK +++EVL EF+EEF + +
Sbjct: 360 AEGKKDYQEVLEEFYEEFKKIV 381